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AndrewCRMartin / absplit

Code to split an antibody PDB file into Fv fragments with their antigens
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pdb6xun_2PH.mar: chain mapping, repeated HETATM, antigen type #16

Closed biochunan closed 1 year ago

biochunan commented 1 year ago

Current 6xun_2PH chain mapping:

REMARK 950 CHAIN-TYPE  LABEL ORIGINAL
REMARK 950 CHAIN L     L     D
REMARK 950 CHAIN H     H     C
REMARK 950 CHAIN A     B     B
SEQRES   1 L  116  GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR

Hapten is in chain G, might be clearer to add 

REMARK 950 CHAIN A     G     G

Also, HETATM lines were repeated in pdb6xun_2PH.mar compared with original PDB file.
In the original PDB file (56 HETATM in chain G)

HETATM section ``` HETATM10097 C1 NAG G 1 -29.496 -5.180 -10.475 1.00 36.52 C HETATM10098 C2 NAG G 1 -29.832 -6.201 -11.559 1.00 39.31 C HETATM10099 C3 NAG G 1 -29.808 -7.616 -10.978 1.00 38.49 C HETATM10100 C4 NAG G 1 -28.488 -7.870 -10.258 1.00 41.60 C HETATM10101 C5 NAG G 1 -28.233 -6.765 -9.239 1.00 37.27 C HETATM10102 C6 NAG G 1 -26.902 -6.879 -8.537 1.00 40.53 C HETATM10103 C7 NAG G 1 -31.220 -5.567 -13.469 1.00 41.32 C HETATM10104 C8 NAG G 1 -32.609 -5.308 -13.974 1.00 31.95 C HETATM10105 N2 NAG G 1 -31.114 -5.920 -12.184 1.00 39.35 N HETATM10106 O1 NAG G 1 -29.506 -3.874 -10.960 1.00 40.28 O HETATM10107 O3 NAG G 1 -29.983 -8.563 -12.027 1.00 40.36 O HETATM10108 O4 NAG G 1 -28.501 -9.130 -9.596 1.00 43.78 O HETATM10109 O5 NAG G 1 -28.241 -5.495 -9.904 1.00 42.13 O HETATM10110 O6 NAG G 1 -26.898 -6.121 -7.335 1.00 47.52 O HETATM10111 O7 NAG G 1 -30.236 -5.459 -14.191 1.00 45.35 O HETATM10112 C1 GAL G 2 -31.215 -9.175 -12.071 1.00 42.90 C HETATM10113 C2 GAL G 2 -31.247 -9.706 -13.512 1.00 37.51 C HETATM10114 C3 GAL G 2 -32.527 -10.446 -13.786 1.00 42.73 C HETATM10115 C4 GAL G 2 -32.776 -11.550 -12.714 1.00 42.43 C HETATM10116 C5 GAL G 2 -32.643 -10.960 -11.320 1.00 36.22 C HETATM10117 C6 GAL G 2 -32.646 -12.011 -10.227 1.00 40.51 C HETATM10118 O2 GAL G 2 -31.213 -8.669 -14.466 1.00 40.36 O HETATM10119 O3 GAL G 2 -32.454 -11.056 -15.060 1.00 41.78 O HETATM10120 O4 GAL G 2 -31.873 -12.626 -12.859 1.00 40.52 O HETATM10121 O5 GAL G 2 -31.411 -10.267 -11.163 1.00 45.23 O HETATM10122 O6 GAL G 2 -32.665 -11.422 -8.956 1.00 45.75 O HETATM10123 C1 SIA G 3 -34.962 -11.322 -15.249 1.00 49.54 C HETATM10124 C2 SIA G 3 -33.522 -11.183 -15.914 1.00 44.89 C HETATM10125 C3 SIA G 3 -33.167 -12.252 -16.951 1.00 41.38 C HETATM10126 C4 SIA G 3 -33.917 -12.060 -18.266 1.00 41.89 C HETATM10127 C5 SIA G 3 -33.714 -10.643 -18.812 1.00 43.46 C HETATM10128 C6 SIA G 3 -34.086 -9.592 -17.742 1.00 43.34 C HETATM10129 C7 SIA G 3 -33.705 -8.128 -18.103 1.00 43.83 C HETATM10130 C8 SIA G 3 -33.978 -7.198 -16.893 1.00 41.99 C HETATM10131 C9 SIA G 3 -34.132 -5.731 -17.279 1.00 36.85 C HETATM10132 C10 SIA G 3 -33.893 -10.170 -21.219 1.00 43.77 C HETATM10133 C11 SIA G 3 -34.798 -10.024 -22.441 1.00 36.77 C HETATM10134 N5 SIA G 3 -34.488 -10.470 -20.038 1.00 43.23 N HETATM10135 O1A SIA G 3 -35.530 -10.201 -15.067 1.00 49.22 O HETATM10136 O1B SIA G 3 -35.368 -12.484 -14.980 1.00 47.67 O HETATM10137 O4 SIA G 3 -33.459 -12.983 -19.265 1.00 46.64 O HETATM10138 O6 SIA G 3 -33.361 -9.864 -16.545 1.00 42.37 O HETATM10139 O7 SIA G 3 -32.347 -8.074 -18.525 1.00 39.67 O HETATM10140 O8 SIA G 3 -35.126 -7.670 -16.184 1.00 47.23 O HETATM10141 O9 SIA G 3 -34.617 -5.662 -18.617 1.00 50.75 O HETATM10142 O10 SIA G 3 -32.683 -10.011 -21.319 1.00 47.56 O HETATM10143 C1 FUC G 4 -27.472 -10.020 -9.794 1.00 40.57 C HETATM10144 C2 FUC G 4 -27.585 -11.275 -8.964 1.00 39.65 C HETATM10145 C3 FUC G 4 -28.633 -12.197 -9.578 1.00 37.71 C HETATM10146 C4 FUC G 4 -28.234 -12.516 -11.003 1.00 39.49 C HETATM10147 C5 FUC G 4 -28.089 -11.205 -11.777 1.00 39.90 C HETATM10148 C6 FUC G 4 -27.564 -11.391 -13.202 1.00 34.71 C HETATM10149 O2 FUC G 4 -27.894 -10.981 -7.630 1.00 32.37 O HETATM10150 O3 FUC G 4 -28.688 -13.423 -8.870 1.00 39.12 O HETATM10151 O4 FUC G 4 -27.002 -13.219 -11.011 1.00 37.02 O HETATM10152 O5 FUC G 4 -27.181 -10.312 -11.113 1.00 38.92 O ```

In pdb6xun_2PH.mar (112 HETATM in chain G)

HETATM section ``` HETATM 3467 C1 SIA G 1 -34.962 -11.322 -15.249 1.00 49.54 C HETATM 3468 C2 SIA G 1 -33.522 -11.183 -15.914 1.00 44.89 C HETATM 3469 C3 SIA G 1 -33.167 -12.252 -16.951 1.00 41.38 C HETATM 3470 C4 SIA G 1 -33.917 -12.060 -18.266 1.00 41.89 C HETATM 3471 C5 SIA G 1 -33.714 -10.643 -18.812 1.00 43.46 C HETATM 3472 C6 SIA G 1 -34.086 -9.592 -17.742 1.00 43.34 C HETATM 3473 C7 SIA G 1 -33.705 -8.128 -18.103 1.00 43.83 C HETATM 3474 C8 SIA G 1 -33.978 -7.198 -16.893 1.00 41.99 C HETATM 3475 C9 SIA G 1 -34.132 -5.731 -17.279 1.00 36.85 C HETATM 3476 C10 SIA G 1 -33.893 -10.170 -21.219 1.00 43.77 C HETATM 3477 C11 SIA G 1 -34.798 -10.024 -22.441 1.00 36.77 C HETATM 3478 N5 SIA G 1 -34.488 -10.470 -20.038 1.00 43.23 N HETATM 3479 O1A SIA G 1 -35.530 -10.201 -15.067 1.00 49.22 O HETATM 3480 O1B SIA G 1 -35.368 -12.484 -14.980 1.00 47.67 O HETATM 3481 O4 SIA G 1 -33.459 -12.983 -19.265 1.00 46.64 O HETATM 3482 O6 SIA G 1 -33.361 -9.864 -16.545 1.00 42.37 O HETATM 3483 O7 SIA G 1 -32.347 -8.074 -18.525 1.00 39.67 O HETATM 3484 O8 SIA G 1 -35.126 -7.670 -16.184 1.00 47.23 O HETATM 3485 O9 SIA G 1 -34.617 -5.662 -18.617 1.00 50.75 O HETATM 3486 O10 SIA G 1 -32.683 -10.011 -21.319 1.00 47.56 O HETATM 3487 C1 FUC G 2 -27.472 -10.020 -9.794 1.00 40.57 C HETATM 3488 C2 FUC G 2 -27.585 -11.275 -8.964 1.00 39.65 C HETATM 3489 C3 FUC G 2 -28.633 -12.197 -9.578 1.00 37.71 C HETATM 3490 C4 FUC G 2 -28.234 -12.516 -11.003 1.00 39.49 C HETATM 3491 C5 FUC G 2 -28.089 -11.205 -11.777 1.00 39.90 C HETATM 3492 C6 FUC G 2 -27.564 -11.391 -13.202 1.00 34.71 C HETATM 3493 O2 FUC G 2 -27.894 -10.981 -7.630 1.00 32.37 O HETATM 3494 O3 FUC G 2 -28.688 -13.423 -8.870 1.00 39.12 O HETATM 3495 O4 FUC G 2 -27.002 -13.219 -11.011 1.00 37.02 O HETATM 3496 O5 FUC G 2 -27.181 -10.312 -11.113 1.00 38.92 O HETATM 3497 C1 NAG G 3 -29.496 -5.180 -10.475 1.00 36.52 C HETATM 3498 C2 NAG G 3 -29.832 -6.201 -11.559 1.00 39.31 C HETATM 3499 C3 NAG G 3 -29.808 -7.616 -10.978 1.00 38.49 C HETATM 3500 C4 NAG G 3 -28.488 -7.870 -10.258 1.00 41.60 C HETATM 3501 C5 NAG G 3 -28.233 -6.765 -9.239 1.00 37.27 C HETATM 3502 C6 NAG G 3 -26.902 -6.879 -8.537 1.00 40.53 C HETATM 3503 C7 NAG G 3 -31.220 -5.567 -13.469 1.00 41.32 C HETATM 3504 C8 NAG G 3 -32.609 -5.308 -13.974 1.00 31.95 C HETATM 3505 N2 NAG G 3 -31.114 -5.920 -12.184 1.00 39.35 N HETATM 3506 O1 NAG G 3 -29.506 -3.874 -10.960 1.00 40.28 O HETATM 3507 O3 NAG G 3 -29.983 -8.563 -12.027 1.00 40.36 O HETATM 3508 O4 NAG G 3 -28.501 -9.130 -9.596 1.00 43.78 O HETATM 3509 O5 NAG G 3 -28.241 -5.495 -9.904 1.00 42.13 O HETATM 3510 O6 NAG G 3 -26.898 -6.121 -7.335 1.00 47.52 O HETATM 3511 O7 NAG G 3 -30.236 -5.459 -14.191 1.00 45.35 O HETATM 3512 C1 GAL G 4 -31.215 -9.175 -12.071 1.00 42.90 C HETATM 3513 C2 GAL G 4 -31.247 -9.706 -13.512 1.00 37.51 C HETATM 3514 C3 GAL G 4 -32.527 -10.446 -13.786 1.00 42.73 C HETATM 3515 C4 GAL G 4 -32.776 -11.550 -12.714 1.00 42.43 C HETATM 3515 C4 GAL G 4 -32.776 -11.550 -12.714 1.00 42.43 C HETATM 3516 C5 GAL G 4 -32.643 -10.960 -11.320 1.00 36.22 C HETATM 3517 C6 GAL G 4 -32.646 -12.011 -10.227 1.00 40.51 C HETATM 3518 O2 GAL G 4 -31.213 -8.669 -14.466 1.00 40.36 O HETATM 3519 O3 GAL G 4 -32.454 -11.056 -15.060 1.00 41.78 O HETATM 3520 O4 GAL G 4 -31.873 -12.626 -12.859 1.00 40.52 O HETATM 3521 O5 GAL G 4 -31.411 -10.267 -11.163 1.00 45.23 O HETATM 3522 O6 GAL G 4 -32.665 -11.422 -8.956 1.00 45.75 O HETATM 3523 C1 SIA G 1 -34.962 -11.322 -15.249 1.00 49.54 C HETATM 3524 C2 SIA G 1 -33.522 -11.183 -15.914 1.00 44.89 C HETATM 3525 C3 SIA G 1 -33.167 -12.252 -16.951 1.00 41.38 C HETATM 3526 C4 SIA G 1 -33.917 -12.060 -18.266 1.00 41.89 C HETATM 3527 C5 SIA G 1 -33.714 -10.643 -18.812 1.00 43.46 C HETATM 3528 C6 SIA G 1 -34.086 -9.592 -17.742 1.00 43.34 C HETATM 3529 C7 SIA G 1 -33.705 -8.128 -18.103 1.00 43.83 C HETATM 3530 C8 SIA G 1 -33.978 -7.198 -16.893 1.00 41.99 C HETATM 3531 C9 SIA G 1 -34.132 -5.731 -17.279 1.00 36.85 C HETATM 3532 C10 SIA G 1 -33.893 -10.170 -21.219 1.00 43.77 C HETATM 3533 C11 SIA G 1 -34.798 -10.024 -22.441 1.00 36.77 C HETATM 3534 N5 SIA G 1 -34.488 -10.470 -20.038 1.00 43.23 N HETATM 3535 O1A SIA G 1 -35.530 -10.201 -15.067 1.00 49.22 O HETATM 3536 O1B SIA G 1 -35.368 -12.484 -14.980 1.00 47.67 O HETATM 3537 O4 SIA G 1 -33.459 -12.983 -19.265 1.00 46.64 O HETATM 3538 O6 SIA G 1 -33.361 -9.864 -16.545 1.00 42.37 O HETATM 3539 O7 SIA G 1 -32.347 -8.074 -18.525 1.00 39.67 O HETATM 3540 O8 SIA G 1 -35.126 -7.670 -16.184 1.00 47.23 O HETATM 3541 O9 SIA G 1 -34.617 -5.662 -18.617 1.00 50.75 O HETATM 3542 O10 SIA G 1 -32.683 -10.011 -21.319 1.00 47.56 O HETATM 3543 C1 FUC G 2 -27.472 -10.020 -9.794 1.00 40.57 C HETATM 3544 C2 FUC G 2 -27.585 -11.275 -8.964 1.00 39.65 C HETATM 3545 C3 FUC G 2 -28.633 -12.197 -9.578 1.00 37.71 C HETATM 3546 C4 FUC G 2 -28.234 -12.516 -11.003 1.00 39.49 C HETATM 3547 C5 FUC G 2 -28.089 -11.205 -11.777 1.00 39.90 C HETATM 3548 C6 FUC G 2 -27.564 -11.391 -13.202 1.00 34.71 C HETATM 3549 O2 FUC G 2 -27.894 -10.981 -7.630 1.00 32.37 O HETATM 3550 O3 FUC G 2 -28.688 -13.423 -8.870 1.00 39.12 O HETATM 3551 O4 FUC G 2 -27.002 -13.219 -11.011 1.00 37.02 O HETATM 3552 O5 FUC G 2 -27.181 -10.312 -11.113 1.00 38.92 O HETATM 3553 C1 NAG G 3 -29.496 -5.180 -10.475 1.00 36.52 C HETATM 3554 C2 NAG G 3 -29.832 -6.201 -11.559 1.00 39.31 C HETATM 3555 C3 NAG G 3 -29.808 -7.616 -10.978 1.00 38.49 C HETATM 3556 C4 NAG G 3 -28.488 -7.870 -10.258 1.00 41.60 C HETATM 3557 C5 NAG G 3 -28.233 -6.765 -9.239 1.00 37.27 C HETATM 3558 C6 NAG G 3 -26.902 -6.879 -8.537 1.00 40.53 C HETATM 3559 C7 NAG G 3 -31.220 -5.567 -13.469 1.00 41.32 C HETATM 3560 C8 NAG G 3 -32.609 -5.308 -13.974 1.00 31.95 C HETATM 3561 N2 NAG G 3 -31.114 -5.920 -12.184 1.00 39.35 N HETATM 3562 O1 NAG G 3 -29.506 -3.874 -10.960 1.00 40.28 O HETATM 3563 O3 NAG G 3 -29.983 -8.563 -12.027 1.00 40.36 O HETATM 3564 O4 NAG G 3 -28.501 -9.130 -9.596 1.00 43.78 O HETATM 3565 O5 NAG G 3 -28.241 -5.495 -9.904 1.00 42.13 O HETATM 3566 O6 NAG G 3 -26.898 -6.121 -7.335 1.00 47.52 O HETATM 3567 O7 NAG G 3 -30.236 -5.459 -14.191 1.00 45.35 O HETATM 3568 C1 GAL G 4 -31.215 -9.175 -12.071 1.00 42.90 C HETATM 3569 C2 GAL G 4 -31.247 -9.706 -13.512 1.00 37.51 C HETATM 3570 C3 GAL G 4 -32.527 -10.446 -13.786 1.00 42.73 C HETATM 3571 C4 GAL G 4 -32.776 -11.550 -12.714 1.00 42.43 C HETATM 3572 C5 GAL G 4 -32.643 -10.960 -11.320 1.00 36.22 C HETATM 3573 C6 GAL G 4 -32.646 -12.011 -10.227 1.00 40.51 C HETATM 3574 O2 GAL G 4 -31.213 -8.669 -14.466 1.00 40.36 O HETATM 3575 O3 GAL G 4 -32.454 -11.056 -15.060 1.00 41.78 O HETATM 3576 O4 GAL G 4 -31.873 -12.626 -12.859 1.00 40.52 O HETATM 3577 O5 GAL G 4 -31.411 -10.267 -11.163 1.00 45.23 O HETATM 3578 O6 GAL G 4 -32.665 -11.422 -8.956 1.00 45.75 O ```
biochunan commented 1 year ago

Antigen type should be Hapten only. This is a case where only a small portin of CDR is close to the antigen protein, though binding activity is primarily between hapten and the CDR loops.

Quote from Literate of PDB 6XUN: "Biomolecular recognition of the tumor-associated carbohydrate antigen CA19-9 by two distinct antibodies using X-ray crystallography."

AndrewCRMartin commented 1 year ago

I am closing this and re-opening as two issues.